I don't really get the square foot garden mixture. I don't think peat moss and vermiculite offer much in the way of nutrients, and in high concentrations are going to dry out fast. I've been filling my beds with what a local quarry calls "veggie mix", which I think is a mix of top soil and compost and maybe something else. But a reputable quarry in your area is going to provide the best soil mixture for growing, IMO. I top my beds off with it every couple years. Alternate years, I throw in composted steer manure, and I continually turn it into the clay soil underneath to get the mixture deeper and deeper every year. Rarely do I fertilize during the growing season, I only water every few days, even when temps get up in the 90's, and I get good results. When it comes time to top off your beds with new soil, I would really consider trying something different. You might find you don't have to water so much and will get better results.

I would say to coax some of these bugs onto a piece of paper and take pictures of them. I have never heard of any herbs like this or any other plants for that matter, dying in a few hours after looking great just hours earlier. The only time I have ever seen anything like that was a few hours after spraying Spectracide weed and grass control. I am talking about the non-selective weed control with diquat dibromide, and on certain weeds it will cause significant visible damage and discoloring within a few hours of its a hot day outside especially. Its possible they just dried out and began wilting.

Its important that we know what kind of plant this is. Might it be one of the cherry laurels? Because those spots look just like a disease called shot hole disease. It starts out as those reddish spots, which eventually die and drop out of the leaf. Shot hole is caused by fungal and/or bacterial agents. Treatment should begin, once you find out for certain what's causing the damage, in the fall. Identification of the plant species is essential. Shot hole could be eliminated right off the bat or determined to be a certainty.....depending upon the plant.

I do not know what the bugs are. Plantlets look ok. I wouldn't complicate rooting so much - I don't see advantage of using paper towels; as you found , it could e annoying trying to get the roots detangled (I never heard of this method). I like it as simple as possible. Most of the time, I just lay leaves on surface of pretty gritty mix and they root and grow in it. I transplant them easily when they are big and start interfering with each other. These were transplanted recently since pot was getting too full:Bunch of leaves started in same pot & gritty mix - 2nd photo as they are now; soon to be given individual pots: